User: Rory Stark

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Rory Stark2.2k
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CRUK, Cambridge, UK
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4 years, 10 months ago
Email:
r*********@cruk.cam.ac.uk

I am Principal Bioinformatics Analyst at the University of Cambridge, leading the Analysis Team in the Bioinformatics Core at Cancer Research UK's Cambridge Institute.

Posts by Rory Stark

<prev • 398 results • page 1 of 40 • next >
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Answer: A: How to judge DESeq2_block and EdgeR_block result
... The difference is most likely due to differences in normalization. the TMM normalization used by edgeR assumes that most of the regions do not change enrichment levels. If this is not the case, the edgeR result will be the incorrect one. You can check by plotting three MA plots: > par(mfrow=c(2 ...
written 4 hours ago by Rory Stark2.2k
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Comment: C: dba.count with pre-defined regions
... Yes, the summits parameter should work to re-center intervals around the point of highest pileup. However I just tested this, and found another bug. I'll check in a fix for DiffBind 2.6.3.  I do have a workaround for you: > TF.counts <- dba.count(TF.peaks, peaks = promoter, score = DBA_SCO ...
written 2 days ago by Rory Stark2.2k
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Answer: A: dba.count with pre-defined regions
... I've had a look and identified a bug, which should be fixed by the end of the week in DiffBind 2.6.2. I see you are using an older version, I can provide a workaround. You just need to pass in the intervals as a data.frame, with the chromosome names (first column) as character strings: > promo ...
written 2 days ago by Rory Stark2.2k
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Answer: A: dba.count with pre-defined regions
... If you can send me the intervals you are passing in as promoter, I can take a look at what is happening. If possible, it would be good to have a copy of the main DBA object TF.peaks -- if this is too large, you can send me a download link (Dropbox or similar). Cheers- Rory rory.stark @ cruk.cam.a ...
written 2 days ago by Rory Stark2.2k
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Answer: A: DiffBind not accessible files in Example data
... Hi Bob- The data for the vignette, including the bam files, are available for download from this page: http://DiffBind.starkhome.com unzip and untar the file at the "Vignette Data: ER binding in tamoxifen resistant and responsive cells (chr18 only)" link, make this your working directory, and you ...
written 5 days ago by Rory Stark2.2k
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Answer: A: DiffBind dba.peakset + bRetrieve=T gives peak scores? or raw counts?
... Hi James- When you call dba.peakset() with bRetrieve=TRUE, you will get back the binding matrix using the score set in dba.count(). So in this case, you will get the TMM normalized scores (with control reads subtracted, and using the full library sizes instead of just the reads in peaks). However ...
written 6 days ago by Rory Stark2.2k
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Answer: A: How to control the size of labels on heatmaps in DiffBind
... The dba.plotHeatmap() function will accept additional parameters for control the plotting of the heatmap. If you look at the help page for gplots::heatmap.2, you can find a bunch of parameters you can set. Specifically, you can set cexRow to change the size of the row labels. Cheers- Rory ...
written 6 days ago by Rory Stark2.2k
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Answer: A: DiffBind remove low count intervals for differential analysis
... Let's take this set-by-step as you raise a number of issues. First is the derivation of the consensus peakset. Your second line of code, calling dba.peakset(), does not determine the consensus peakset used for counting. I’m a little confused as to how you used this result, as passing it to dba.coun ...
written 7 days ago by Rory Stark2.2k
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Answer: A: DiffBind Heatmap Omitting Results?
... By default, the maxSites parameter of dba.plotHeatmap() is set to maxSites=1000. This means it will only use the "top" 1,000 intervals (the 1,000 sites with the lowest FDR values when you specify a contrast). You can increase the value of maxSites to plot more sites but it will take longer (the comp ...
written 7 days ago by Rory Stark2.2k
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Answer: A: Using HOMER called peaks in DiffBind
... You can use the pos2bed.pl utility that comes with HOMER. There is a discussion of this here: https://support.bioconductor.org/p/63923/ See particularly Gord's answer near the top. Cheers- Rory P.S. We still have an "add support for HOMER peak format" feature in our list of to-do, maybe someday ...
written 7 days ago by Rory Stark2.2k

Latest awards to Rory Stark

Scholar 6 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Guru 7 months ago, received more than 100 upvotes.
Popular Question 7 months ago, created a question with more than 1,000 views. For a diffBind problem
Scholar 7 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Popular Question 7 months ago, created a question with more than 1,000 views. For a diffBind problem
Scholar 10 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Scholar 10 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Autobiographer 15 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 20 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Scholar 20 months ago, created an answer that has been accepted. For A: What does dba.PCA in DiffBind exactly do?
Scholar 20 months ago, created an answer that has been accepted. For A: DiffBind matrix of values
Scholar 20 months ago, created an answer that has been accepted. For A: ChIPQC and/or Diffbind - retrieving normalized read counts for peaks from single
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Work with GRanges objects in DiffBind
Scholar 22 months ago, created an answer that has been accepted. For A: What does dba.PCA in DiffBind exactly do?
Scholar 2.0 years ago, created an answer that has been accepted. For A: What does dba.PCA in DiffBind exactly do?
Scholar 2.1 years ago, created an answer that has been accepted. For A: What does dba.PCA in DiffBind exactly do?
Scholar 2.2 years ago, created an answer that has been accepted. For A: Work with GRanges objects in DiffBind
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: diffBind correlation plot
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Work with GRanges objects in DiffBind
Scholar 2.2 years ago, created an answer that has been accepted. For A: diffBind correlation plot
Scholar 2.2 years ago, created an answer that has been accepted. For A: Clarification about the functionality of dba.count and dba.analyze
Scholar 2.2 years ago, created an answer that has been accepted. For A: subset of samples from dba object in DiffBind
Scholar 2.4 years ago, created an answer that has been accepted. For A: problem with characters in chromosome names in DiffBind dba
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: diffBind correlation plot
Scholar 2.5 years ago, created an answer that has been accepted. For A: diffBind correlation plot

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